FH Molecules Research Articles

Morphological, Microstructural, and In Situ Chemical Characteristics of Siderite Produced by Iron-Reducing Bacteria.

Dissimilatory iron-reducing bacteria (DIRB) oxidize organic matter or hydrogen and reduce ferric iron to form Fe(II)-bearing minerals, such as magnetite and siderite. However, compared with magnetite, which was extensively studied, the mineralization process and mechanisms of siderite remain unclear. Here, with the combination of advanced electron microscopy and synchrotron-based scanning transmission X-ray microscopy (STXM) approaches, we studied in detail the morphological, structural, and chemical features of biogenic siderite via a growth experiment with Shewanella oneidensis MR-4. Results showed that along with the growth of cells, Fe(II) ions were increasingly released into solution and reacted with CO32- to form micrometer-sized siderite minerals with spindle, rod, peanut, dumbbell, and sphere shapes. They are composed of many single-crystal siderite plates that are fanned out from the center of the particles. Additionally, STXM revealed Fh and organic molecules inside siderite. This suggests that the siderite crystals might assemble around a Fh-organic molecule core and then continue to grow radially. This study illustrates the biomineralization and assembly of siderite by a successive multistep growth process induced by DIRB, also provides evidences that the distinctive shapes and the presence of organic molecules inside might be morphological and chemical features for biogenic siderite.

Performance of a one-parameter correlation factor for transcorrelation: Study on a series of second row atomic and molecular systems.

In this work, we investigate the performance of a recently proposed transcorrelated (TC) approach based on a single-parameter correlation factor [E. Giner, J. Chem. Phys. 154, 084119 (2021)] for systems involving more than two electrons. The benefit of such an approach relies on its simplicity as efficient numerical-analytical schemes can be set up to compute the two- and three-body integrals occurring in the effective TC Hamiltonian. To obtain accurate ground state energies within a given basis set, the present TC scheme is coupled to the recently proposed TC-full configuration interaction quantum Monte Carlo method [Cohen et al., J. Chem. Phys. 151, 061101 (2019)]. We report ground state total energies on the Li-Ne series, together with their first cations, computed with increasingly large basis sets and compare to more elaborate correlation factors involving electron-electron-nucleus coordinates. Numerical results on the Li-Ne ionization potentials show that the use of the single-parameter correlation factor brings on average only a slightly lower accuracy (1.2 mH) in a triple-zeta quality basis set with respect to a more sophisticated correlation factor. However, already using a quadruple-zeta quality basis set yields results within chemical accuracy to complete basis set limit results when using this novel single-parameter correlation factor. Calculations on the H2O, CH2, and FH molecules show that a similar precision can be obtained within a triple-zeta quality basis set for the atomization energies of molecular systems.

The Structure and Dynamics of the Chains of Hydrogen Bonds of Hydrogen Fluoride Molecules Inside Carbon Nanotubes

It is shown by molecular dynamics that hydrogen fluoride molecules inside single-wall carbon nanotubes with a diameter D < 0.85 nm form flat zigzag chains of F–H···F–H···F–H··· hydrogen bonds. The chains that are the closest to the chain of hydrogen bonds of OH hydroxyl groups in structure form hydrogen fluoride molecules inside nanotubes with the chirality indices (6, 6) and (10, 0). In such open nanotubes with narrowed down ends, the chains of (FH)N hydrogen bonds may fully fill in their internal cavity, thus forming a structure resistant to thermal vibrations in a wide range of temperatures. Stationary orientational defects localized on three to four chain units which divide the parts of the chain with the opposite orientations of the FH molecules can exist in the chains. (FH)N ∈ CNT (6, 6) and (FH)N ∈ CNT (10, 0) molecular complexes can act as proton-conducting “nanowires,” in which the external nanotube acts as the winding (insulation) which protects and stabilizes the internal proton-conducting chain of (FH)N.

Структура и динамика цепочек водородных связей молекул фтористого водорода внутри углеродных нанотрубок

Using the method of molecular dynamics, it was shown that hydrogen fluoride molecules inside single-wall carbon nanotubes with a diameter D&lt;0.85 nm form flat zigzag chains of hydrogen bonds F–H∙ ∙ ∙F–H∙ ∙ ∙F–H∙ ∙ ∙ . The chains structurally closest to the chain of hydrogen bonds of hydroxyl groups OH form hydrogen fluoride molecules inside nanotubes with a chirality index (6,6) and (10,0). In such open nanotubes with narrowed edges, hydrogen bond chains (FH) _N can completely fill their internal cavity forming a structure that is resistant to thermal fluctuations in a wide temperature range. The chains can have stationary orientation defects localized on 3-4 chain links separating parts of the chain having the opposite directions of FH molecules. The molecular complexes (FH)_N∈CNT(6,6) and (FH)_N∈CNT(10,0) can play the role of proton-conducting nanowires, in which the outer nanotube serves as a external winding (insulation) that protects and stabilizes the inner proton-conducting chain (FH)_N.

Anticooperativity of FH···Cl- hydrogen bonds in [FH)n Cl]- clusters (n = 1…6).

The change of cooperativity of FH···Cl- hydrogen bonds upon sequential addition of up to six FH molecules to the Cl- first coordination sphere is investigated. The geometry of clusters [(FH) n Cl]- (n = 1…6) was calculated (CCSD/aug-cc-pVDZ) and compared with [(FH) n F]- clusters. The geometry is determined by the symmetry-driven electrostatic requirements and also by the fact that formation of each new FH···Cl- bond creates a depression in the chlorine's electron cloud on the opposite side of Cl- (σ-hole), which limits the range of directions available for subsequent H-bond formation. The mutual influence of FH···Cl- hydrogen bonds is anticooperative-the addition of each FH molecule weakens H-bonds by 23-16% and decreases their covalent character (as seen by LMO-EDA decomposition and QTAIM analysis). Anticooperativity effects could be tracked by spectroscopic parameters (frequency of local HF mode νFH , chemical shift δH , spin-spin coupling constants 1 JFH , 1h JHCl , 2h JFCl and nuclear quadrupolar constants χ18F , χD , and χ35Cl . © 2019 Wiley Periodicals, Inc.

Hydrogen and Halogen Bonding in Cyclic FH(4- n):FCl n Complexes, for n = 0-4.

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the six unique cyclic quaternary complexes FH:FH:FH:FH, FH:FH:FH:FCl, FH:FH:FCl:FCl, FH:FCl:FH:FCl, FH:FCl:FCl:FCl, and FCl:FCl:FCl:FCl stabilized by F-H···F hydrogen bonds and F-Cl···F halogen bonds. The binding energies of these complexes decrease as the number of FH molecules decreases, and therefore as the number of hydrogen bonds decreases, indicating that hydrogen bonds are primarily responsible for stabilities. Nonadditivities of binding energies are synergistic for complexes with 4, 3, and 2 FH molecules, but antagonistic for those with 1 and 0 FH molecules. In addition to depending on changes in F-F, F-H, and F-Cl distances, complex binding energies are also influenced by two sets of angular parameters. These include the external F-F-F angles which must sum to 360° in these cyclic structures, and the internal H-F-F angles for hydrogen bonds and F-Cl-F angles for halogen bonds, which measure the deviation from linearity of these bonds. Transition structures present the barriers to converting an equilibrium structure to an equivalent equilibrium structure on the potential surfaces. These barriers increase as the number of FH molecules decreases. EOM-CCSD spin-spin coupling constants 2h J(F-F) across hydrogen bonds in complexes tend to increase with decreasing F-F distance. They increase dramatically in transition structures, but show no dependence on the F-F distance. The one-bond coupling constants 1h J(F-H) are relatively small and negative in complexes, increase dramatically, and are positive in transition structures. 1 J(F-H) values are greatest for the covalent F-H bond. Coupling constants 1x J(F-Cl) across halogen bonds are relatively small and positive in complexes, and increase dramatically in transition structures. The largest values of 1 J(F-Cl) are found for covalent bonds.

Unusual acid-base properties of the P4 molecule in hydrogen-, halogen-, and pnicogen-bonded complexes.

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate hydrogen bonding, halogen bonding, and pnicogen bonding involving tetrahedral P4 and the FH, ClH, and FCl molecules. P4 has three unique interaction sites: at a vertex (designated the P1 atom); at an edge (the P2-P3 bond); and at the P2-P3-P4 face. The uniqueness of molecular P4 is its ability to act as an electron donor and an electron acceptor at the same site, except for the P2-P3 bond, which is only an electron donor. FCl and FH form five different complexes with P4, but ClH forms only three. The type of complex formed and its binding energy depend on both the interaction site of molecular P4 and the interacting molecule. For all complexes with FH, ClH, and FCl, the binding energies at a given site with the P4 molecule acting as the base are greater than the binding energies when P4 is the acid. Thus, P4 is a better electron donor than an electron acceptor. Charge-transfer interactions and EOM-CCSD spin-spin coupling constants across hydrogen, halogen, and pnicogen bonds are reported for all of the P4 complexes. Relative to 1J(Pi-Pj) in molecular P4, 1J(P1-P2) coupling constants decrease in absolute value and 1J(P2-P3) coupling constants increase in pnicogen-bonded complexes and the complex with FCl that has a PF halogen bond. Absolute values of 1J(P1-P2) increase and those of 1J(P2-P3) decrease in hydrogen-bonded complexes and complexes with PCl halogen bonds. 1J(P1-P2) and 1J(P2-P3) exhibit a single linear correlation with the corresponding Pi-Pj distances.

Multiple Hartree-Fock Solutions of Systems Constituted with First Line Atoms: BH and FH molecules using the Double Zeta Base

Multiple Hartree-Fock Solutions of Systems Constituted with First Line Atoms: BH and FH molecules using the Double Zeta Base

The interaction between factor H and Von Willebrand factor.

Complement factor H (fH) is a plasma protein that regulates activation of the alternative pathway, and mutations in fH are associated with a rare form of thrombotic microangiopathy (TMA), known as atypical hemolytic uremic syndrome (aHUS). A more common TMA is thrombotic thrombocytopenic purpura, which is caused by the lack of normal ADAMTS-13-mediated cleavage of von Willebrand factor (VWF). We investigated whether fH interacts with VWF and affects cleavage of VWF. We found that factor H binds to VWF in plasma, to plasma-purified VWF, and to recombinant A1 and A2 domains of VWF as detected by co-immunoprecipitation (co-IP) and surface plasmon resonance assays. Factor H enhanced ADAMTS-13-mediated cleavage of recombinant VWF-A2 as determined by quantifying the cleavage products using Western-blotting, enhanced cleavage of a commercially available fragment of VWF-A2 (FRETS-VWF73) as determined by fluorometric assay, and enhanced cleavage of ultralarge (UL) VWF under flow conditions as determined by cleavage of VWF-platelet strings attached to histamine stimulated endothelial cells. Using recombinant full-length and truncated fH molecules, we found that the presence of the C-terminal half of fH molecule is important for binding to VWF-A2 and for enhancing cleavage of the A2 domain by ADAMTS-13. We conclude that factor H binds to VWF and may modulate cleavage of VWF by ADAMTS-13.

Influence of Hydrogen Bonds on the P···P Pnicogen Bond.

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the influence of F-H···F hydrogen bonds on the P···P pnicogen bond in complexes nFH:(PH2F)2 for n = 1-3. The formation of F-H···F hydrogen bonds leads to a shortening of the P-P distance, a lengthening of the P-F distance involved in the hydrogen bond, a strengthening of the P···P interaction, and changes in atomic populations, NMR (31)P chemical shieldings, and (1p)J(P-P) coupling constants. The magnitude of these changes depends on the number of FH molecules and their positions in the complex and are relatively modest except for complexes 2FH:(PH2F)2 and 3FH:(PH2F)2 that have all FH molecules hydrogen bonded to the same F-atom. For these two complexes, (1p)J(P-P) decreases as the P-P distance decreases and approaches the value of (1)J(P-P) for P2H4. The dramatic changes in these two complexes reflect the changing nature of the hydrogen bonds and the pnicogen bond. Thus, the complex 3FH:(PH2F)2 acquires ion-pair character represented as [3(FH)F(-):(H2P-PH2F)(+)], and the P···P pnicogen bond acquires significant covalent character. These changes are observed to a lesser extent in 2FH:(PH2F)2.

Multi-Jastrow trial wavefunctions for electronic structure calculations with quantum Monte Carlo

A new type of electronic trial wavefunction suitable for quantum Monte Carlo calculations of molecular systems is presented. In contrast with the standard Jastrow-Slater form built with a unique global Jastrow term, it is proposed to introduce individual Jastrow factors attached to molecular orbitals. Such a form is expected to be more physical since it allows to describe differently the local electronic correlations associated with various molecular environments (1s-core orbitals, 3d-magnetic orbitals, localized two-center sigma-orbitals, delocalized pi-orbitals, atomic lone pairs, etc.). In contrast with the standard form, introducing different Jastrow terms allows us to change the nodal structure of the wavefunction, a point which is important in the context of building better nodes for more accurate fixed-node diffusion Monte Carlo (FN-DMC) calculations. Another important aspect resulting from the use of local Jastrow terms is the possibility of defining and preoptimizing local and transferable correlated units for building complex trial wavefunctions from simple parts. The practical aspects associated with the computation of the intricate derivatives of the multi-Jastrow trial function are presented in detail. Some first illustrative applications for atoms of increasing size (O, S, and Cu) and for the potential energy curve and spectroscopic constants of the FH molecule are presented. In the case of the copper atom, the use of the multi-Jastrow form at the variational Monte Carlo level has allowed us to improve significantly the value of the total ground-state energy (about 75% of the correlation energy with only one determinant and three atomic orbital Jastrow factors). In the case of the FH molecule (fluorine hydride), it has been found that the multi-Jastrow nodes lead to an almost exact FN-DMC value of the dissociation energy [D(0)=-140.7(4) kcal/mol instead of the estimated nonrelativistic Born-Oppenheimer exact value of -141.1], which is not the case with standard nodes, D(0)=-138.3(4) kcal/mol.

Halogen and hydrogen bonding to the Br atom in complexes of FBr

A computational study predicts a number of stable, unusual halogen- and hydrogen-bonded complexes involving FBr, NCH, and FH. Starting from the linear halogen-bonded FBr...NCH dimer, increasingly more stable complexes are obtained by the successive hydrogen bonding of one to three FH molecules to the lone pairs on the Br atom of FBr to form a trimer, tetramer, and pentamer. A hexamer is obtained from the pentamer by the bonding of FH to the F atom of FBr. The combined halogen and hydrogen bonding gives rise to a large computed zero-point corrected binding energy of 98 kJ/mol for the hexamer at the MP2/6-31++G(d,p) level of theory.

Automated calculation of anharmonic vibrational contributions to first hyperpolarizabilities: Quadratic response functions from vibrational configuration interaction wave functions

Quadratic response functions are derived and implemented for a vibrational configuration interaction state. Combined electronic and vibrational quadratic response functions are derived using Born-Oppenheimer vibronic product wave functions. Computational tractable expressions are derived for determining the total quadratic response contribution as a sum of contributions involving both electronic and vibrational linear and quadratic response functions. In the general frequency-dependent case this includes a new and more troublesome type of electronic linear response function. Pilot calculations for the FH, H(2)O, CH(2)O, and pyrrole molecules demonstrate the importance of vibrational contributions for accurate comparison to experiment and that the vibrational contributions in some cases can be very large. The calculation of transition properties between vibrational states is combined with sum-over-states expressions for analysis purposes. On the basis of this some simple analysis methods are suggested. Also, a preliminary study of the effect of finite lifetimes on quadratic response functions is presented.

Species-specificity of Neisseria gonorrhoeae infection: Do human complement regulators contribute?

Neisseria gonorrhoeae is the causative agent of gonorrhea, a disease restricted to humans. Complement forms a key arm of the innate immune system that combats gonococcal infections. N. gonorrhoeae uses its outer membrane porin (Por) molecules to bind complement down-regulatory proteins, C4b-binding protein (C4BP) and factor H (fH), to evade killing by human complement. In addition, sialylation of gonococcal lipooligosaccharide (LOS) also enables N. gonorrhoeae to bind fH. Strains of N. gonorrhoeae that resist killing by human serum complement are killed by serum from rodent, lagomorph and primate species, which cannot be readily infected experimentally with this organism and whose C4BP and/or fH molecules do not bind to N. gonorrhoeae. Serum resistance of gonococci is restored in these sera by human C4BP and/or fH. Direct binding specificity of human and chimpanzee C4BP and human fH to gonococci may explain, in part, species-specific restriction of natural gonococcal infection and address why Por1B, but not Por1A containing gonococcal strains, have been successful in experimental chimpanzee infection. Our findings may help to improve animal models for gonorrhea while also having implications in the choice of complement sources to evaluate neisserial vaccine candidates.

Ab Initio EOM-CCSD Spin−Spin Coupling Constants for Hydrogen-Bonded Formamide Complexes: Bridging Complexes with NH3, (NH3)2, H2O, (H2O)2, FH, and (FH)2

EOM-CCSD spin-spin coupling constants across hydrogen bonds have been computed for complexes in which NH3, H2O, and FH molecules and their hydrogen-bonded dimers form bridging complexes in the amide region of formamide. The formamide one-bond N-H coupling constant [(1)J(N-H)] across N-H...X hydrogen bonds increases in absolute value upon complexation. The signs of the one-bond coupling constants (1h)J(H-X) indicate that these complexes are stabilized by traditional hydrogen bonds. The two-bond coupling constants for hydrogen bonds with N-H as the donor [(2h)J(N-X)] and the carbonyl oxygen as the acceptor [(2h)J(X-O)] increase in absolute value in the formamide/dimer relative to the corresponding formamide/monomer complex as the hydrogen bonds acquire increased proton-shared character. The largest changes in coupling constants are found for complexes of formamide with FH and (FH)2, suggesting that bridging FH monomers and dimers in particular could be useful NMR spectroscopic probes of amide hydrogen bonding.

Molecular one‐electron properties using the multireference Hartree–Fock CI method

AbstractThe recently introduced multireference Hartree–Fock configuration interaction (MRHFCI) method has been applied to the calculation of the dipole moment of the LiH, BH, FH, CO, and H2O molecules. The results obtained indicate that MRHFCI wave functions, much more compact but of the same quality of the orthogonal full CI ones, can provide better dipole moments than the corresponding full CI wave functions. The value of the dipole moments obtained with the MRHFCI wave functions is quite insensitive to the choice of the HF references but the same is not true for the electronic energy. Therefore, further studies are necessary to develop a criterion for selecting a set of HF references which could provide the best values of energy and dipole moment. Also, it would be important to verify if other one‐electron properties can be computed with the same degree of accuracy obtained for the dipole moments. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Atomic basis sets optimization using the generalized simulated annealing approach: New basis sets for the first row elements

AbstractAtomic basis sets equivalent to the standard STO‐3G and STO‐6G ones were optimized for the elements of the first row using the generalized simulated annealing (GSA) approach. The atomic energies obtained with the new basis sets are substantially better than the ones obtained with the standard ones. The new basis sets were tested for several diatomic and triatomic molecules, at different levels of calculation. For the molecules at their geometries of equilibrium, the energies obtained with the GSA optimized basis are in general much better than the respective ones obtained with the standard basis. However, for molecules containing hydrogen atoms, the best results, either at the HF or CI level of calculation, are obtained with a combination of the new and the standard bases, which depend on the nature of the other atoms of the molecule. The analysis of the potential energy surfaces for the LiH, BH, and FH molecules showed that the new basis provide a better description of these molecules in all regions of the respective surfaces, although the equilibrium bond distances. The results are quite encouraging and clearly indicate that basis set of DZ and TZ quality better than the standard ones can probably be generated by the GSA approach. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008

Many-body Brillouin–Wigner second-order perturbation theory using a multireference formulation: an application to bond breaking in the diatomic hydrides BH and FH∥

The multireference, state specific, second-order, Brillouin–Wigner perturbation theory is presented. A posteriori corrections are made which in the case of a single reference function recover the well-known formula of second-order many-body perturbation theory, i.e. Møller–Plesset ‘MP2’ theory, and in the multireference case yields a state specific multireference second-order Rayleigh–Schrödinger perturbation theory. Applications to the bond breaking processes in the ground states of the BH and FH molecules are described using basis sets for which the corresponding full configuration interaction calculations are possible. Multireference Brillouin–Wigner coupled cluster calculations, in the CCSD approximation, are presented for these diatomic molecules using the same basis sets. ∥This paper is dedicated to Professor Andrzej J. Sadlej, Nicholas Copernicus University, Toruń, on the occasion of his 65th birthday.

GSA algorithm applied to electronic structure II: UHF‐GSA method

AbstractIn this paper we propose a stochastic algorithm to investigate the real unrestricted Hartree–Fock problem. The approach is based on a global optimization method, the Generalized Simulated Annealing. The main characteristic of this method is that it enables the mapping of the electronic hyper‐surface in such a way as to guarantee that the absolute minimum of the functional in focus will be achieved. We tested this methodology by determining the Hartree–Fock ground‐state of the H2, LiH, BH, CH+, OH−, FH, CO, N2, BeH2, H2O, NH3, HCHO, CH4, CH, NH, CH2, NH2, OH and O2 molecules using minimal, double‐zeta, triple‐zeta and with polarization basis sets. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

On using Fourier series and Legendre polynomials as angular basis sets for nonrotating triatomic molecules

The numerical properties of quantum grid methods applying the Fourier series and Legendre polynomials as angular basis sets for triatomic molecule calculations are compared. The three-dimensional time-dependent wavepacket calculations ( J = 0) by using relaxation technique are performed to obtain the lowest vibrational eigenvalues of ground electronic states of OBrO and van der Waals Na⋯FH molecules. For the OBrO molecule with a deep well potential along bending mode, the numerical models using the Fourier series with fast Fourier transform technique as the angular basis set are very efficient. And the Legendre polynomials is appropriate to describe the Na⋯FH molecule with a floppy potential along bending mode.